Identification of QTL Responsible for an Economically Valuable Soybean Seed Oil Trait Using Next-Generation Sequencing Methods.

Soybean seed oil is primarily composed of unsaturated fatty acids, which are oxidatively unstable. Soybean oil with elevated saturated fatty acid content is desirable both to increase the stability in the oil and eliminate the need for chemical hydrogenation, which produces trans fats. Stearic acid (C18:0) is a prime target for breeders as it has been shown to have no negative effect on low-density lipoproteins (LDL) as do other saturated fats. The elevated stearic acid trait has been previously identified to be determined by mutations in a single stearoyl-ACP desaturase (SACPD-C) gene, which can elevate stearic acid levels from ~3% (wild type) to ~15%. In order to fully evaluate the genetic basis for the elevated stearic acid trait, we developed a RIL population using two elevated stearic acid mutants, A6 (~28% stearic acid) and 194D (~12% stearic acid). At F3:4, we observed transgressive segregation for stearic acid content, which alludes to the action of more than one gene. We obtained dense SNP marker data using the Genotyping-by-Sequencing (GBS) method and performed QTL analysis for the elevated seed stearic acid trait. One major effect QTL was identified, due to the SACPD-C gene on chromosome 14, which explained ~48.7% of the variation in the trait (P<.001). We also identified two minor effect QTL on chromosome 2 and 4 (~5% and 6.8%, respectively) that contribute to seed stearic acid content additively with the major effect QTL on chromosome 14. Our results will be immensely useful in working toward the complete understanding of this economically valuable seed oil trait.